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RNA category is based on mRNA expression levels in the analyzed samples (RNA assay description). The categories include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected. RNA category is calculated separately for data imported from The Genotype-Tissue Expression project (GTEX), FANTOM5 Consortium (FANTOM5) and internally generated Human Protein Atlas (HPA) data.
Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.
Evidence at protein level
Protein expressioni
A summary of the overall protein expression pattern across the analyzed normal tissues. The summary is based on knowledge-based annotation.
"Estimation of protein expression could not be performed. View primary data." is shown for genes analyzed with a knowledge-based approach where available RNA-seq and gene/protein characterization data has been evaluated as not sufficient in combination with immunohistochemistry data to yield a reliable estimation of the protein expression profile.
Cytoplasmic expression in most tissues, highly abundant in epithelial cells.
IMMUNOHISTOCHEMISTRY DATA RELIABILITY
Data reliability descriptioni
Standardized explanatory sentences with additional information required for full understanding of the knowledge-based expression profile.
Caution, targets protein from more than one gene. External characterization data supports antibody staining.
Reliability scorei
Reliability score (score description), divided into Enhanced, Supported, Approved, or Uncertain, is evaluated in normal tissues and based on consistency between antibody staining pattern, available RNA-Seq and gene/protein characterization data, as well as similarity between independent antibodies targeting the same protein.
Below is an overview of RNA and protein expression data generated in the Human Protein Atlas project. Analyzed tissues are divided into color-coded groups according to which functional features they have in common. For each group, a list of included tissues is accessed by clicking on group name, group symbol, RNA bar, or protein bar. Subsequent selection of a particular tissue in this list links to the image data page.
Images of selected tissues give a visual summary of the protein expression profile furthest to the right.
The gray human body provides links to a histology dictionary when clicking on any part of the figure.
RNA expression (TPM)i
RNA-seq results generated in HPA are reported as number of transcripts per million (TPM). Each bar represents the highest expression score found in a particular group of tissues. The assay is described more in detail in Assays & Annotation.
Protein expression (score)i
Each bar represents the highest expression score found in a particular group of tissues. Protein expression scores are based on a best estimate of the "true" protein expression from a knowledge-based annotation, described more in detail under Assays & annotation. For genes where more than one antibody has been used, a collective score is set displaying the estimated true protein expression.
Protein expression data is shown for each of the 44 tissues. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. Mouse-over function shows protein score for analyzed cell types in a selected tissue. To access image data click on tissue name or bar. Annotation of protein expression is described in detail in Assays & annotation.
For genes with available protein data for which a knowledge-based annotation gave inconclusive results, no protein expression data is displayed in the protein expression data overview. However, all immunohistochemical images are still available and the annotation data can be found under Primary data.
Organ
Expression
Alphabetical
RNA EXPRESSION OVERVIEWi
RNA expression overview shows RNA-data from three different sources: Internally generated Human Protein Atlas (HPA) RNA-seq data, RNA-seq data from the Genotype-Tissue Expression (GTEx) project and CAGE data from FANTOM5 project. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar.
HPA dataseti
HPA dataset RNA-seq tissue data is reported as mean TPM (transcripts per million), corresponding to mean values of the different individual samples from each tissue. Color-coding is based on tissue groups, each consisting of tissues with functional features in common. To access sample data, click on tissue name or bar. The RNA-seq assay is described in detail in Assays & Annotation.
RNA tissue category HPA HPA RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
GTEx dataseti
GTEx dataset RNA-seq data is reported as median RPKM (reads per kilobase per million mapped reads), generated by the Genotype-Tissue Expression (GTEx) project. More information can be found in Assays & Annotation.
RNA tissue category GTEx GTEx RNA tissue category (category description) is calculated based on mRNA expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
FANTOM5 dataseti
FANTOM5 dataset Tissue data obtained through Cap Analysis of Gene Expression (CAGE) are reported as Tags Per Million, generated by the FANTOM5 project. More information can be found in Assays & Annotation.
RNA tissue category FANTOM5 FANTOM5 RNA tissue category (category description) is calculated based on gene expression levels across all tissues and include: tissue enriched, group enriched, tissue enhanced, expressed in all, mixed and not detected.
Organ
Expression
Alphabetical
RNA tissue category: Expressed in all
GENE INFORMATIONi
Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.
Gene name
RAC1 (HGNC Symbol)
Synonyms
p21-Rac1, Rac-1, TC-25
Description
Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) (HGNC Symbol)
Entrez gene summary
The protein encoded by this gene is a GTPase which belongs to the RAS superfamily of small GTP-binding proteins. Members of this superfamily appear to regulate a diverse array of cellular events, including the control of cell growth, cytoskeletal reorganization, and the activation of protein kinases. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.
At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.
Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more).
The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more).
If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.
Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
RAC1-001
RAC1-002
PROTEIN INFORMATIONi
The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.
The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.
The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.
The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
P63000 [Direct mapping] Ras-related C3 botulinum toxin substrate 1 A4D2P1 [Target identity:100%; Query identity:100%] Ras-related C3 botulinum toxin substrate 1 (Rho family, small GTP binding protein Rac1); Ras-related C3 botulinum toxin substrate 1 (Rho family, small GTP binding protein Rac1), isoform CRA_a; Ras-related C3 botulinum toxin substrate 1 isoform Rac1; cDNA FLJ30431 fis, clone BRACE2008968, highly similar to Ras-related C3 botulinum toxin substrate 1; cDNA FLJ75553, highly similar to Homo sapiens ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) (RAC1), transcript variant Rac1, mRNA
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Predicted intracellular proteins RAS pathway related proteins Cancer-related genes Candidate cancer biomarkers Mutated cancer genes Mutational cancer driver genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Missense Mutations COSMIC Frameshift Mutations Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)
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GO:0000166 [nucleotide binding] GO:0001934 [positive regulation of protein phosphorylation] GO:0003924 [GTPase activity] GO:0005515 [protein binding] GO:0005525 [GTP binding] GO:0005622 [intracellular] GO:0005737 [cytoplasm] GO:0005789 [endoplasmic reticulum membrane] GO:0005802 [trans-Golgi network] GO:0005829 [cytosol] GO:0005884 [actin filament] GO:0005886 [plasma membrane] GO:0005925 [focal adhesion] GO:0006928 [movement of cell or subcellular component] GO:0006954 [inflammatory response] GO:0007155 [cell adhesion] GO:0007160 [cell-matrix adhesion] GO:0007264 [small GTPase mediated signal transduction] GO:0007596 [blood coagulation] GO:0008361 [regulation of cell size] GO:0009611 [response to wounding] GO:0009653 [anatomical structure morphogenesis] GO:0010310 [regulation of hydrogen peroxide metabolic process] GO:0010592 [positive regulation of lamellipodium assembly] GO:0010811 [positive regulation of cell-substrate adhesion] GO:0016020 [membrane] GO:0019899 [enzyme binding] GO:0030027 [lamellipodium] GO:0030032 [lamellipodium assembly] GO:0030036 [actin cytoskeleton organization] GO:0030041 [actin filament polymerization] GO:0030168 [platelet activation] GO:0030334 [regulation of cell migration] GO:0030667 [secretory granule membrane] GO:0031012 [extracellular matrix] GO:0031295 [T cell costimulation] GO:0031529 [ruffle organization] GO:0031996 [thioesterase binding] GO:0032707 [negative regulation of interleukin-23 production] GO:0034446 [substrate adhesion-dependent cell spreading] GO:0035025 [positive regulation of Rho protein signal transduction] GO:0035556 [intracellular signal transduction] GO:0036464 [cytoplasmic ribonucleoprotein granule] GO:0038095 [Fc-epsilon receptor signaling pathway] GO:0038096 [Fc-gamma receptor signaling pathway involved in phagocytosis] GO:0042470 [melanosome] GO:0043065 [positive regulation of apoptotic process] GO:0043197 [dendritic spine] GO:0043312 [neutrophil degranulation] GO:0048010 [vascular endothelial growth factor receptor signaling pathway] GO:0048013 [ephrin receptor signaling pathway] GO:0048261 [negative regulation of receptor-mediated endocytosis] GO:0048870 [cell motility] GO:0050690 [regulation of defense response to virus by virus] GO:0051022 [Rho GDP-dissociation inhibitor binding] GO:0051056 [regulation of small GTPase mediated signal transduction] GO:0051496 [positive regulation of stress fiber assembly] GO:0051668 [localization within membrane] GO:0051894 [positive regulation of focal adhesion assembly] GO:0060071 [Wnt signaling pathway, planar cell polarity pathway] GO:0060263 [regulation of respiratory burst] GO:0070062 [extracellular exosome] GO:0071526 [semaphorin-plexin signaling pathway] GO:0090023 [positive regulation of neutrophil chemotaxis] GO:0101003 [ficolin-1-rich granule membrane] GO:1900026 [positive regulation of substrate adhesion-dependent cell spreading]
P63000 [Direct mapping] Ras-related C3 botulinum toxin substrate 1 A4D2P0 [Target identity:100%; Query identity:100%] Ras-related C3 botulinum toxin substrate 1 (Rho family, small GTP binding protein Rac1); Ras-related C3 botulinum toxin substrate 1 (Rho family, small GTP binding protein Rac1), isoform CRA_e; cDNA FLJ77333, highly similar to Homo sapiens ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) (RAC1), transcript variant Rac1b, mRNA
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SCAMPI predicted membrane proteins Predicted intracellular proteins RAS pathway related proteins Cancer-related genes Candidate cancer biomarkers Mutated cancer genes Mutational cancer driver genes COSMIC somatic mutations in cancer genes COSMIC Somatic Mutations COSMIC Missense Mutations COSMIC Frameshift Mutations Protein evidence (Kim et al 2014) Protein evidence (Ezkurdia et al 2014)